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- PDB-1cw3: HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE COMPLEXED WITH NAD+ AN... -

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Basic information

Entry
Database: PDB / ID: 1cw3
TitleHUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE COMPLEXED WITH NAD+ AND MN2+
ComponentsMITOCHONDRIAL ALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DINUCLEOTIDE FOLD
Function / homology
Function and homology information


Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation / carboxylesterase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / NAD binding / electron transfer activity / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / extracellular exosome
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.58 Å
AuthorsNi, L. / Zhou, J. / Hurley, T.D. / Weiner, H.
Citation
Journal: Protein Sci. / Year: 1999
Title: Human liver mitochondrial aldehyde dehydrogenase: three-dimensional structure and the restoration of solubility and activity of chimeric forms.
Authors: Ni, L. / Zhou, J. / Hurley, T.D. / Weiner, H.
#1: Journal: Structure / Year: 1997
Title: Structure of mitochondrial aldehyde dehydrogenase: the genetic component of ethanol aversion.
Authors: Steinmetz, C.G. / Xie, P. / Weiner, H. / Hurley, T.D.
History
DepositionAug 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
B: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
C: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
D: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
E: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
F: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
G: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
H: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,70232
Polymers431,7618
Non-polymers5,94124
Water19,5821087
1
A: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
B: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
C: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
D: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,85116
Polymers215,8804
Non-polymers2,97112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26630 Å2
ΔGint-155 kcal/mol
Surface area56960 Å2
MethodPISA
2
E: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
F: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
G: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
H: MITOCHONDRIAL ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,85116
Polymers215,8804
Non-polymers2,97112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26370 Å2
ΔGint-145 kcal/mol
Surface area57190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.4, 176.3, 102.0
Angle α, β, γ (deg.)90, 94.7, 90
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
MITOCHONDRIAL ALDEHYDE DEHYDROGENASE / E.C.1.2.1.3 / ALDHI / ALDH-E2


Mass: 53970.090 Da / Num. of mol.: 8
Fragment: COMPLETE MATURE SEQUENCE (DOES NOT INCLUDE MITOCHONDRIAL LEADER SEQUENCE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1087 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 100 MM ACES, PH 6.4, 100 MM GUANIDINE-HCL, 2 MM NAD+, 4 MM DTT, 16% PEG 6000, 8 MG/ML ENZYME SOAKED WITH 8 MM MNCL2 FOR 2 DAYS, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein11
2100 mMACES12
3100 mMguanidine-HCl12
42 mMNAD+12
53 mMdithiothreitol12
617 %(w/v)PEG600012

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.58→45 Å / Num. all: 112240 / Num. obs: 102859 / % possible obs: 91.6 % / Redundancy: 2.15 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.6
Reflection shellResolution: 2.58→2.68 Å / Redundancy: 1.51 % / Rmerge(I) obs: 0.287 / % possible all: 64.3
Reflection
*PLUS
Lowest resolution: 45 Å / Num. measured all: 221417
Reflection shell
*PLUS
% possible obs: 64.3 % / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.58→45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: STANDARD X-PLOR WEIGHTS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 7234 7 %RANDOM
Rwork0.175 ---
all0.18 102859 --
obs0.18 102859 91.6 %-
Refinement stepCycle: LAST / Resolution: 2.58→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30384 0 368 1087 31839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.28
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 45 Å / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.58 Å / Lowest resolution: 2.68 Å

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